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Showing :
Microarray
•
reset
1
vote
5
replies
2.2k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.3 years ago by
chandlerjd58
▴ 10
1
vote
4
replies
2.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 18 months ago by
Sarah
• 0
2
votes
2
replies
2.5k
views
Biostatistician Position: UMass Medical School
Microarray
Microarray
written 16.9 years ago by
David Lapointe
▴ 190
0
votes
2
replies
723
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray
Alignment
Biostrings
written 12 months ago by
sandmann.t
▴ 70
1
vote
2
replies
916
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
13 months ago
Abdul
▴ 20
2
votes
2
replies
684
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
13 months ago
Abdul
▴ 20
0
votes
2
replies
711
views
Full list of differential genes not obtained in topTable
Microarray
GEOquery
topTable
limma
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Ankita
• 0
1
vote
6
replies
1.8k
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 9 months ago by
Gordon Smyth
50k • written 3.7 years ago by
linouhao
▴ 20
2
votes
2
replies
673
views
Question about avereps function of limma
avereps
probes
average
limma
Microarray
updated 14 months ago by
Gordon Smyth
50k • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
0
replies
644
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
15 months ago
jsharif
• 0
0
votes
1
reply
650
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 15 months ago by
James W. MacDonald
66k • written 15 months ago by
Aleksandra
• 0
0
votes
2
replies
955
views
Remove batch effect between microarray data
Microarray
DifferentialExpression
limma
MicroarrayData
removebatcheffect
16 months ago
dqt
• 0
0
votes
2
replies
732
views
Celfiles not reading in
Microarray
written 16 months ago by
Oluwaseun
• 0
1
vote
2
replies
6.3k
views
How to convert Illumina HT_12_v4 annotation
convert
R
annotation
microarray
illumina human ht-12 v4
updated 17 months ago by
snijesh
▴ 20 • written 6.4 years ago by
p_donchev84
• 0
6
votes
6
replies
1.5k
views
Too many differentially expressed miRNA with limma
limma
miRNA
Microarray
18 months ago
Sara
▴ 10
0
votes
17
replies
2.3k
views
Advice for the analysis of microarray data with limma
Microarray
MicroarrayData
limma
updated 15 months ago by
Gordon Smyth
50k • written 19 months ago by
Sam
• 0
0
votes
1
reply
694
views
Compare different cell lines with tissues using limma
limma
MicroarrayData
Microarray
Agilent
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
Sam
• 0
0
votes
8
replies
1.5k
views
Finding differentially expressed genes in a prospective cohort study
limma
MicroarrayData
Microarray
23 months ago
YC
• 0
2
votes
13
replies
4.5k
views
Error in using r
microarray
updated 23 months ago by
17545106088
• 0 • written 7.6 years ago by
azhar
• 0
0
votes
4
replies
1.1k
views
Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray
DifferentialExpression
23 months ago
S
• 0
1
vote
2
replies
840
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
23 months ago
Mikołaj Mierzejewski
• 0
1
vote
2
replies
1.1k
views
Affymetrix analysis of microarray by using Limma
limma
MicroarrayData
Microarray
Affymetrix
23 months ago
Mikołaj Mierzejewski
• 0
4
votes
10
replies
1.9k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219
Microarray
oligo
AffymetrixChip
2.0 years ago
Yang Shi
▴ 10
3
votes
4
replies
1.7k
views
Quantile Normalization after rma or not?
limma
Microarray
oligo
2.0 years ago
Yang Shi
▴ 10
2
votes
2
replies
822
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db
Microarray
oligo
2.0 years ago
Yang Shi
▴ 10
2
votes
5
replies
1.9k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi
Microarray
2.0 years ago
nhaus
▴ 40
0
votes
2
replies
797
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db
MicroarrayData
Microarray
pd.clariom.d.human
2.1 years ago • updated 2.0 years ago
amir.rakhimov.b
• 0
0
votes
2
replies
1.2k
views
Time course experiment using limma
limma
Multi-levelExperiments
Microarray
2.1 years ago
Wendy
• 0
0
votes
12
replies
1.6k
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
2.1 years ago
Adam
• 0
0
votes
0
replies
634
views
Error in svd(X) when using edge lrt (or odp) function.
edge
Microarray
longitudinal
2.2 years ago
emily
• 0
1
vote
7
replies
7.7k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray
normalization
oligo HTA
updated 2.2 years ago by
Harald
• 0 • written 5.3 years ago by
RV
▴ 10
2
votes
5
replies
1.9k
views
Adjust for base line gene expression in limma model
limma
Microarray
updated 2.4 years ago by
Gordon Smyth
50k • written 2.4 years ago by
S
• 0
4
votes
6
replies
1.2k
views
RMA on different disease labels
rma
background
microarray
normalization
updated 2.5 years ago by
James W. MacDonald
66k • written 2.6 years ago by
Joshua
• 0
1
vote
1
reply
1.2k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray
GEOquery
cancerdata
MicroarrayData
updated 2.7 years ago by
James W. MacDonald
66k • written 2.7 years ago by
Caitlin
▴ 50
5
votes
2
replies
2.3k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray
limma
DifferentialExpression
updated 21 months ago by
Gordon Smyth
50k • written 2.8 years ago by
Nikshay
▴ 10
0
votes
1
reply
1.2k
views
Re-normalize microarray dataset in R
microarray
quantile
expression
R
Normalization
updated 2.8 years ago by
Konstantinos Yeles
▴ 80 • written 2.9 years ago by
mohammedtoufiq91
▴ 10
3
votes
5
replies
1.7k
views
Use of arrayWeights with two treatment groups
Microarray
arrays
limma
MicroarrayData
updated 2.9 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Emma
• 0
1
vote
1
reply
1.3k
views
How do I adjust for other factors in Limma differential expression analysis?
limma
Microarray
MicroarrayData
arrays
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.0 years ago by
Emma
• 0
1
vote
2
replies
1.4k
views
RUV4 for microarrays
RUV4
RUV
Microarray
3.1 years ago • updated 3.0 years ago
Antonio
• 0
0
votes
2
replies
2.1k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD
pcaMethods
MicroarrayData
Microarray
3.1 years ago
waiyin0923
• 0
0
votes
1
reply
883
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip
Microarray
affymetrix
updated 3.1 years ago by
Guido Hooiveld
★ 4.0k • written 3.1 years ago by
Pierre-Alex
• 0
1
vote
2
replies
1.3k
views
How to quantile normalize arraystar lncRNA microarray data?
limma
Microarray
3.1 years ago
a.deb
• 0
3
votes
3
replies
1.4k
views
Weird MAplot with DEGs lying along the diagonals
limma
Microarray
AgilentChip
MA-plot
Normalization
3.2 years ago
FedeXander
• 0
0
votes
2
replies
1.7k
views
WGCNA - Outliers after creating sample tree
MicroarrayData
WGCNA
Microarray
3.3 years ago • updated 3.2 years ago
jpwl2
• 0
6
votes
4
replies
1.3k
views
Limma outputs different results for same sample?
topTable
MicroarrayData
ebayes
limma
Microarray
3.3 years ago
snijesh
▴ 20
1
vote
2
replies
1.4k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions
3factors
limma
Microarray
3.3 years ago
Dan
▴ 20
3
votes
9
replies
1.5k
views
limma analysis when only Cy5 was used
MicroarrayData
limma
Microarray
3.3 years ago
Daniel.Schnell
• 0
0
votes
1
reply
1.3k
views
Creating a model matrix for three age groups using two-colour arrays
Microarray
BRAIN
Microarray
BRAIN
updated 3.3 years ago by
Gordon Smyth
50k • written 15.5 years ago by
Carthika Luxmanan
▴ 10
5
votes
8
replies
2.5k
views
how to annotate arrays
affy
annotation
microarray
oligo
updated 3.5 years ago by
James W. MacDonald
66k • written 8.8 years ago by
ben_cossins
• 0
0
votes
1
reply
1.1k
views
Normalisation of protein micro array data using VSN
microarray
normalization
protein
updated 3.5 years ago by
Wolfgang Huber
★ 13k • written 4.9 years ago by
keniajin
• 0
50 results • Page
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Comment: ChAMP installation issue
by
Tahirah
• 0
Thanks a lot. But unfortunately it didn't work. I guess I will have to wait until ChAMP becomes available for version 3.19 In the meantime …
Comment: Slightly different count plots from R and spreadsheet
by
boczniak767
▴ 720
Thank you, but now I have six black and six red boxes (3 black, 3 red, 3 black, 3 red) whereas for each timepoint I have two experimental v…
Comment: Slightly different count plots from R and spreadsheet
by
Michael Love
42k
I added `col` so you can see the different groups. I just want you to be able to see the raw data so you can infer which plot is correct.
Comment: Slightly different count plots from R and spreadsheet
by
boczniak767
▴ 720
Thank you, the code you provided gives boxplots for each data-point for pooled samples?
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
xuz
• 0
Could you try the following code and see whether you have any errors mf="MouseMethylation-12v1-0_A2.csv" manifest=readmanifest(mf) What …
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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★ 6.5k
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Gordon Smyth
50k
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